In-depth Characterization and Analysis of Mutational Signatures ('ICAMS')

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Documentation for package ‘ICAMS’ version 2.1.2

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all.abundance K-mer abundances.
AnnotateDBSVCF Add sequence context and transcript information to an in-memory DBS VCF.
AnnotateIDVCF Add sequence context to an in-memory ID (insertion/deletion) VCF, and confirm that they match the given reference genome.
AnnotateSBSVCF Add sequence context and transcript information to an in-memory SBS VCF.
as.catalog Create a catalog from a 'matrix', 'data.frame', or 'vector'.
Canonicalize1Del Given a deletion and its sequence context, categorize it.
catalog.row.order Standard order of row names in a catalog.
catalog.row.order.sp Standard order of row names in a catalog.
CatalogRowOrder Standard order of row names in a catalog.
Collapse144CatalogTo78 "Collapse" a catalog.
Collapse1536CatalogTo96 "Collapse" a catalog.
Collapse192CatalogTo96 "Collapse" a catalog.
CollapseCatalog "Collapse" a catalog.
FindDelMH Return the length of microhomology at a deletion.
FindMaxRepeatDel Return the number of repeat units in which a deletion is embedded.
gene.expression.data.HepG2 Example gene expression data from two cell lines.
gene.expression.data.MCF10A Example gene expression data from two cell lines.
GeneExpressionData Example gene expression data from two cell lines.
GetMutectVAF Extract the VAFs (variant allele frequencies) and read depth information from a VCF file.
GetStrelkaVAF Extract the VAFs (variant allele frequencies) and read depth information from a VCF file.
GetVAF Extract the VAFs (variant allele frequencies) and read depth information from a VCF file.
ICAMS ICAMS: In-depth Characterization and Analysis of Mutational Signatures
MutectVCFFilesToCatalog Create SBS, DBS and Indel catalogs from Mutect VCF files
MutectVCFFilesToCatalogAndPlotToPdf Create SBS, DBS and Indel catalogs from Mutect VCF files and plot them to PDF
MutectVCFFilesToZipFile Create a zip file which contains catalogs and plot PDFs from Mutect VCF files
PlotCatalog Plot *one* spectrum or signature.
PlotCatalogToPdf Plot catalog to a PDF file.
PlotTransBiasGeneExp Plot transcription strand bias with respect to gene expression values.
PlotTransBiasGeneExpToPdf Plot transcription strand bias with respect to gene expression values to a PDF file.
ReadAndSplitMutectVCFs Read and split Mutect VCF files.
ReadAndSplitStrelkaSBSVCFs Read and split Strelka SBS VCF files.
ReadCatalog Read catalog.
ReadStrelkaIDVCFs Read Strelka ID (small insertion and deletion) VCF files.
revc Reverse complement every string in 'string.vec'.
StrelkaIDVCFFilesToCatalog Create ID (small insertion and deletion) catalog from Strelka ID VCF files
StrelkaIDVCFFilesToCatalogAndPlotToPdf Create ID (small insertion and deletion) catalog from Strelka ID VCF files and plot them to PDF
StrelkaIDVCFFilesToZipFile Create a zip file which contains ID (small insertion and deletion) catalog and plot PDF from Strelka ID VCF files
StrelkaSBSVCFFilesToCatalog Create SBS and DBS catalogs from Strelka SBS VCF files.
StrelkaSBSVCFFilesToCatalogAndPlotToPdf Create SBS and DBS catalogs from Strelka SBS VCF files and plot them to PDF
StrelkaSBSVCFFilesToZipFile Create a zip file which contains catalogs and plot PDFs from Strelka SBS VCF files
trans.ranges.GRCh37 Transcript ranges data
trans.ranges.GRCh38 Transcript ranges data
trans.ranges.GRCm38 Transcript ranges data
TranscriptRanges Transcript ranges data
TransformCatalog Transform between counts and density spectrum catalogs and counts and density signature catalogs.
VCFsToDBSCatalogs Create DBS catalogs from VCFs
VCFsToIDCatalogs Create ID (small insertion and deletion) catalog from ID VCFs
VCFsToSBSCatalogs Create SBS catalogs from SBS VCFs
WriteCatalog Write a catalog